tbuckley/cabot-search huggingface dataset:
Prion infection modulates hematopoietic stem/progenitor cell fate through cell-autonomous and non-autonomous mechanisms
Authors: Hyun-Jaung Sim, Yong-Chan Kim, Govinda Bhattarai, Sae-Young Won, Jeong-Chae Lee, Byung-Hoon Jeong, Sung-Ho Kook
Journal: Leukemia (2023)

Abstract Studies of PrP C -derived prion disease generally focus on neurodegeneration. However, little is known regarding the modulation of hematopoietic stem progenitor cells (HSPCs) that express PrP C in prion infection. Among bone marrow (BM) hematopoietic cells, hematopoietic stem cells (HSCs) strongly express PrP C . A bioassay revealed the presence of misfolded prion protein (PrP Sc ) in BM cells derived from prion-infected mice; these BM cells demonstrated reproducible prion infectivity. At 5 months after infection with ME7, mice exhibited a significant decrease in the number of HSPCs. This decrease was mainly driven by increased apoptotic cell death, rather than cell cycle progression and senescence, in PrP C -positive but not PrP C -negative HSPC populations through a cell-autonomous mechanism. Notably, both PrP C -positive and PrP C -negative HSCs underwent cellular senescence, as indicated by high levels of senescence-associated factors and deficits in repopulation and self-renewal capacities at 7 months after infection. Senescence of HSCs occurred in the ME7-impaired BM microenvironment with aging phenotypes through non-cell autonomous mechanisms. These data provide novel evidence that prion infection differentially modulates HSC fate through both cell-autonomous and non-autonomous mechanisms.
Information for Persons Who Are Immunocompromised Regarding Prevention and Treatment of SARS-CoV-2 Infection in the Context of Currently Circulating Omicron Sublineages — United States, January 2023
Authors: Pragna Patel, Evelyn Twentyman, Emily Koumans, Hannah Rosenblum, Shannon Griffin-Blake, Brendan Jackson, Sara Vagi
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

As of January 20, 2023, >90% of circulating SARS-CoV-2 variants in the United States, specifically Omicron BQ.1, BQ.1.1, XBB, and XBB.1.5 sublineages, are unlikely to be susceptible to the combined monoclonal antibodies, tixagevimab and cilgavimab (Evusheld) used for preexposure prophylaxis against SARS-CoV-2 infection (1). The Food and Drug Administration announced on January 26, 2023, that Evusheld is not currently authorized for preexposure prophylaxis against SARS-CoV-2 infection in the United States (2). It is important that persons who are moderately to severely immunocompromised,* those who might have an inadequate immune response to COVID-19 vaccination, and those with contraindications to receipt of COVID-19 vaccines, exercise caution and recognize the need for additional preventive measures (Box). In addition, persons should have a care plan that includes prompt testing at the onset of COVID-19 symptoms and rapid access to antivirals if SARS-CoV-2 infection is detected.
PP01.16 Improving Access to Early Palliative Care Delivery for Patients with an Advanced Thoracic Malignancy Through an Embedded Onco-Palliative Clinic Model
Authors: J. Agne, E. Bertino, K. Gast, M. Grogan, S. Janse, J. Benedict, C. Presley
Journal: Journal of Thoracic Oncology (2023)
PP01.78 Brain Metastasis in Patients With KRAS Mutant Advanced NSCLC Receiving Docetaxel: Pooled Clinical Trial Data Analysis
Authors: J. Aptekar, R. Jain, B. Korytowsky, A. Shafquat, J. Hendershot, A. Talwai, Y. Itzkovich, S. Padda
Journal: Journal of Thoracic Oncology (2023)
PP01.09 Genotypic Characteristics and Resistance Mutations in Advanced ALK+ NSCLC: The ALK-PATHFINDER Study
Authors: R. López Castro, A. Insa Molla, E. Esteban González, A. Gómez Rueda, D. Isla Casado, I. Barneto Aranda, C. Bayona Antón, M. Majem Tarruella, S. Peralta Muñoz, R. García Campelo, J. Bosch Barrera, O. J. Juan Vidal, R. Bernabé Caro, D. Vicente Baz, R. Gordo Flores, N. Carrizo Mijarra, I. Ferrer Sánchez, M.E. López Muñoz, S. Ponce Aix
Journal: Journal of Thoracic Oncology (2023)
OA01.08 Clinical Response to Tepotinib According to Circulating Tumor (ct)DNA Biomarkers in Patients with Advanced/Metastatic NSCLC with High-level MET Amplification (METamp) Detected by Liquid Biopsy (LBx)
Authors: X. Le, L.G. Paz-Ares, J. Van Meerbeeck, S. Viteri, C. Cabrera-Galvez, D.V. Baz, Y.-C. Kim, J.-H. Kang, C. Stroh, D. Juraeva, R. Bruns, G. Otto, A. Johne, P.K. Paik
Journal: Journal of Thoracic Oncology (2023)
PP01.08 Circulating Genetically Abnormal Cells Predicts Risk of Lung Cancer in Individuals with Indeterminant Pulmonary Nodules
Authors: B.A. Katchman, S. Tahvilian, J.D. Kuban, D.F. Yankelevitz, D. Leventon, C.I. Henschke, J. Zhu, L. Baden, R. Yip, F.R. Hirsch, R. Reed, A. Brown, A. Muldoon, M. Trejo, M.J. Donovan, P.C. Pagano
Journal: Journal of Thoracic Oncology (2023)
PP01.77 EMERGE 402: Real-world Characteristics and Safety of Lurbinectedin in Small-cell Lung Cancer (SCLC)
Authors: D. Schreeder, F. Badin, S. Dakhil, P. Lammers, M. Patel, D. Slater, J. Migas, N. Naveh, A. Boccuti, R. Hanvesakul, W. Li, B. Halmos
Journal: Journal of Thoracic Oncology (2023)
PP01.73 Time from Biopsy to Treatment Initiation at an Academic Hospital and Affiliate Hospitals: Overall Survival Analysis
Authors: C. Vakkalagadda, D. Dressler, P. Silberman, Z. Sun, M. Kocherginsky, Y. Boumber, Y. Kwang Chae, N. Mohindra, A. Ragam, J. Patel
Journal: Journal of Thoracic Oncology (2023)
PP01.40 Target Lesion Response and Outcomes in Patients Treated with Brigatinib vs Crizotinib in ALTA-1L
Authors: D Ross Camidge, H. Ryun Kim, M.J. Ahn, James CH. Yang, J.-Y. Han, M.J. Hochmair, K.H. Lee, A. Delmonte, M.R. Garcia Campelo, D.-W. Kim, F. Griesinger, E. Felip, R. Califano, A.I. Spira, M. Thomas, S.N. Gettinger, M. Tiseo, Y. Liu, P. Zhang, S. Popat
Journal: Journal of Thoracic Oncology (2023)
mTORC1 syndrome (TorS): unified paradigm for diabetes/metabolic syndrome
Authors: Jacob Bar-Tana
Journal: Trends in Endocrinology and Metabolism (2023)

'Glucolipotoxicity' and 'insulin resistance' are claimed to drive type 2 diabetes (T2D) and the non-glycemic diseases of the metabolic syndrome (MetS) (obesity, dyslipidemia, hypertension). In line with that, glycemic and/or insulin control are considered to be primary goal in treating T2D/MetS. However, recent standard-of-care (SOC) treatments of T2D, initially designed to control T2D hyperglycemia, appear now to alleviate the cardio-renal and non-glycemic diseases of T2D/MetS independently of glucose lowering and insulin resistance, and in non-T2D patients altogether, calling for an alternative unifying pathophysiology/treatment paradigm for T2D/MetS. This opinion article proposes to replace the current 'glucolipotoxic/insulin-resistance' paradigm of T2D/MetS with an 'mammalian target of rapamycin complex 1 (mTORC1) syndrome' (TorS) paradigm, implying an exhaustive cohesive disease entity driven by an upstream hyperactive mTORC1, and which includes diabetic hyperglycemia, diabetic dyslipidemia, hypertension, diabetic macrovascular and microvascular disease, non-alcoholic fatty liver disease, some cancers, neurodegeneration, polycystic ovary syndrome (PCOS), psoriasis, and others. The TorS paradigm may account for the insulin-resistant glycemic context of TorS, combined with response to insulin of the non-glycemic diseases of TorS. The TorS paradigm may account for the efficacy of current antidiabetic SOC treatments in diabetic and nondiabetic patients. Most importantly, the TorS paradigm may generate novel treatments for TorS.
Single‐cell analysis of allergic diseases
Authors: Yasutaka Mitamura, Cezmi A. Akdis
Journal: Allergy (2023)

BOX 1 Single-cellmultiomicstechnologies 1. Genome: To investigate the correlation between genomic alterations, such as mutation, and their linked transcriptomic changes in single cells G&T-seq, TARGET-seq 2. Proteome: To explore the link between proteome profiling, such as surface markers, and transcriptome CITE-seq, REAP-seq, PEA/STA, PLAYR, RAID 3. Epigenome: To demonstrate the links between epigenome, such as methylation and open chromatin sites, and transcriptome scM&T-seq, scTrio-seq, scNMT-seq, sci-CAR, SNARE-seq Genome and transcriptome (G&T), cellular indexing of transcriptomes and epitopes (CITE), RNA expression and protein (REAP), proximity extension assay/specific RNA target amplification (PEA/STA), proximity ligation assay for RNA (PLAYR), RNA and immunodetection (RAID), singlecell (sc), methylome and transcriptome (M&T), triple omics (Trio), nucleosome, methylation and transcription (NMT), combinatorial indexing chromatin accessibility and mRNA expression sequencing (sci-CAR), single-nucleus chromatin accessibility and mRNA (SNARE).
Reply to Benjamin Pradere, Giuseppe Basile, and Thomas Seisen’s Letter to the Editor re: Maria S. Lindgren, Eric Hansen, Nessn Azawi, Anna M. Nielsen, Lars Dyrskjøt, Jørgen B. Jensen. DaBlaCa-13 Study: Oncological Outcome of Short-term, Intensive Chemoresection with Mitomycin in Nonmuscle Invasive Bladder Cancer: Primary Outcome of a Randomized Controlled Trial. J Clin Oncol 2023;41:2,206–11
Authors: Maria S. Lindgren, Jørgen B. Jensen
Journal: European Urology (2023)
The evolving role of quantitative actigraphy in clinical sleep medicine
Authors: Claudio Liguori, Samantha Mombelli, Mariana Fernandes, Marco Zucconi, Giuseppe Plazzi, Luigi Ferini-Strambi, Giancarlo Logroscino, Nicola Biagio Mercuri, Marco Filardi
Journal: Sleep Medicine Reviews (2023)

Actigraphy has a consolidated role in Insomnia and Circadian Rhythm Sleep-Wake Disorders (CRSWD) and recent studies have highlighted the use of actigraphy for narcolepsy and REM sleep behaviour disorder (RBD). This review aims at summarising the results of studies published over the last decade regarding the use of actigraphy. Thirty-five studies proved eligible, and results were analysed separately for insomnia, narcolepsy and RBD. Actigraphy showed to consistently differentiate insomnia patients from healthy controls. Furthermore, the application of advanced analytical techniques has been shown to provide both unique insights into the physiology of insomnia and sleep misperception and to improve the specificity of actigraphy in detecting wakefulness within sleep periods. Regarding narcolepsy, several studies showed that actigraphy can detect peculiar sleep/wake disruption and the effects of pharmacological treatments. Finally, although the number of studies in RBD patients is still limited, the available evidence indicates a reduced amplitude of the activity pattern, sleep-wake rhythm dysregulation and daytime sleepiness. Therefore, the potential use of these markers as predictors of phenoconversion should be further explored. In conclusion, quantitative actigraphy presents a renewed interest when considering the possibility of using actigraphy in clinical sleep medicine to diagnose, monitor, and follow sleep disorders other than CRSWD.
Moderate‐to‐severe atopic dermatitis in different age groups treated with dupilumab in China
Authors: Xiaoting Song, Bo Liu, Tingting Luan, Shuanglu Liao, Yen Tan, Chengyue Peng, Zuotao Zhao
Journal: Allergy (2023)

Appendix S1. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The genomic landscape and clonal evolutionary trajectory of classical hairy cell leukemia
Authors: Luz Yurany Moreno Rueda, Dean Bryant, William J. Tapper, Nicola J. Weston-Bell, David C. Wedge, Naser Ansari-Pour, Surinder S. Sahota
Journal: Leukemia (2023)

In understanding clonal evolution in cancer, whole genome sequencing (WGS) provides unparalleled data that can be leveraged to derive tumor phylogenies.Specifically, estimates of the cancer cell fraction (CCF), that is the fraction of tumor cells bearing a set of somatic mutations, is highly informative by defining which mutations are clonal and are associated with the most recent common ancestor (MRCA) of all tumor cells, and which mutations occur subclonally as later events.By clustering all observed somatic mutations based on their CCF and subsequent phylogenetic tree inference, derived tumor phylogenies provide an even more detailed view of the tumor history than mere single point estimates of CCF of driver variants, as they determine the relative order of all events and infer evolutionary trajectories.These evolutionary trajectories inform which driver genes are early events in tumorigenesis, that dysregulate cellular molecular pathways critical to clonal proliferation.HCL is a rare chronic B-cell lymphoproliferative disorder characterized by the presence of small tumor cells with hairylike projections and membrane ruffles, which do not resemble any known peripheral normal B-cell subpopulation [1].Typical classical HCL (HCLc) universally bears a coding BRAF V600E mutation, making it a rare monogenic cancer.A large number of additional exonic mutations have been observed in HCLc, but none are pervasive across all tumors [2].A conundrum, however, has remained that activating BRAF mutations also occur in benign tumors, including precursors to malignant carcinoma [3], to suggest that additional genetic drivers trigger malignant transformation.In HCLc, it is not yet known whether other driver mutations may arise in noncoding regions to cooperate with BRAF V600E in driving tumorigenesis.To probe this, we carried out WGS in HCLc for the first time, and reconstructed subclonal genomic architecture and inferred evolutionary trajectories.Our data provide, firstly, a comprehensive mapping of the whole genome in HCLc including noncoding regions to yield BRAF V600E as the sole universal lesion in disease.Secondly, and importantly, clonal evolutionary analyses suggested that BRAF V600E
Outcome prediction in myelodysplastic neoplasm undergoing hematopoietic cell transplant in the molecular era of IPSS-M
Authors: Carmelo Gurnari, Nico Gagelmann, Anita Badbaran, Hussein Awada, Danai Dima, Simona Pagliuca, Maud D’Aveni-Piney, Enrico Attardi, Maria Teresa Voso, Raffaella Cerretti, Christine Wolschke, Marie Thérèse Rubio, Jaroslaw P. Maciejewski, Nicolaus Kröger
Journal: Leukemia (2023)
A Biomimetic Lubricating Nanosystem with Responsive Drug Release for Osteoarthritis Synergistic Therapy
Authors: Cheng Li, Peiwei Gong, Mianran Chao, Juan Li, Liyan Yang, Yan Huang, Dandan Wang, Jianxi Liu, Zhe Liu
Journal: Advanced Healthcare Materials (2023)

Abstract Osteoarthritis (OA) is associated with lubrication failure of articular cartilage and severe inflammatory response of joint capsule. Synergistic therapy combining joint lubrication and anti‐inflammation emerges as a novel treatment of OA. In this study, bioinspired by ultralow friction of natural articular synovial fluid and mussel adhesion chemistry, a biomimetic nanosystem with dual functions of enhanced lubrication and stimuli‐responsive drug release is developed. A dopamine mediated strategy realizes one step biomimetic grafting of hyaluronic acid (HA) on fluorinated graphene. The polymer modified sheets exhibit highly efficient near‐infrared absorption, and show steady lubrication with a long time under various working conditions, in which the coefficient of friction is reduced by 75% compared to H 2 O. Diclofenac sodium (DS) with a high loading capacity of 29.2% is controllably loaded, and responsive and sustained drug release is adjusted by near‐infrared light. Cell experiments reveal that the lubricating nanosystem is taken up by endocytosis, and anti‐inflammation results confirm that the nanosystem inhibits osteoarthritis deterioration by upregulating cartilage anabolic gene and downregulating catabolic proteases and pain‐related gene. This work proposes a promising biomimetic approach to integrate polymer modified fluorinated graphene as a dual‐functional nanosystem for effective synergistic therapy of OA.
The histone demethylase JMJD2C constitutes a novel NFE2 target gene that is required for the survival of JAK2V617F mutated cells
Authors: Anne Marie Staehle, Jan Caspar Peeken, Georg Vladimirov, Mirjam Elisabeth Hoeness, Sarolta Bojtine Kovacs, Nikolaos Karantzelis, Albert Gruender, Christoph Koellerer, Jonas Samuel Jutzi, Heike Luise Pahl, Hans Felix Staehle
Journal: Leukemia (2023)

Abstract The transcription factor NFE2 is overexpressed in most patients with myeloproliferative neoplasms (MPN). Moreover, mutations in NFE2, found in a subset of MPN patients, strongly predispose for transformation to acute leukemia. Transgenic mice overexpressing NFE2 as well as mice harboring NFE2 mutations display an MPN phenotype and spontaneously develop leukemia. However, the molecular mechanisms effecting NFE2-driven leukemic transformation remain incompletely understood. Here we show that the pro-leukemic histone demethylase JMJD2C constitutes a novel NFE2 target gene. JMJD2C expression is elevated in MPN patients as well as in NFE2 transgenic mice. Moreover, we show that loss of JMJD2C selectively impairs proliferation of JAK2 V617F mutated cells. Our data suggest that JMJD2C represents a promising drug target in MPN and provide a rationale for further investigation in preclinical and clinical settings.
The Case of Baby Fae
Authors: Olga Jonasson
Journal: JAMA (1985)

Appearing in this issue ofThe Journalis the first full scientific report of the "case of Baby Fae"—cardiac xenotransplantation in a neonate. Many emotional editorial comments about this case have appeared in the lay press and in respected scientific publications. Critical editorial commentary by peers, based on an impartial analysis of the scientific gathering of the facts, is now appropriate. The infant, born prematurely with hypoplastic left heart syndrome, an invariably fatal form of congenital heart disease, received the heart of a young female baboon in an uncomplicated surgical procedure on Oct 26, 1984. At the time of transplantation the infant was critically ill, and urgent surgical intervention was required if she was to survive even for a brief interval. Based on his own evaluation of the alternatives, Dr Bailey had offered xenotransplantation to the mother. The alternatives were three: a risky palliative surgical procedure, the Norwood procedure,<sup>1</sup>
Genetic Defects in Lipoprotein Metabolism
Authors: Robert W. Mahley
Journal: JAMA (1991)

Certain proteins (called apolipoproteins B and E) on the surface of lipoprotein particles are responsible for mediating the binding of cholesterol-rich particles to specific lipoprotein receptors on the surface of cells and represent a major pathway controlling blood cholesterol levels. Three important disorders of lipoprotein metabolism, which provide insights into the molecular mechanisms responsible for the elevation of specific atherogenic lipoproteins, are the following: (1) Type III hyperlipoproteinemia results from specific mutations in apolipoprotein E that prevent the normal binding of chylomicron remnants and very-lowdensity lipoprotein remnants to lipoprotein receptors. Patients with this disorder who have elevated levels of these remnant lipoproteins develop atherosclerosis. (2) Familial defective apolipoprotein B-100 results from a single amino acid substitution in apolipoprotein B that prevents low-density lipoprotein from binding normally to the low-density lipoprotein receptor and elevates plasma cholesterol levels. (3) Familial hypercholesterolemia, which results in elevated levels of plasma low-density lipoprotein and premature atherosclerosis, is caused by a variety of mutations in the low-density lipoprotein receptor that interfere with the normal binding of lipoproteins to this receptor. These observations not only provide insights into the mechanisms responsible for normal lipoprotein metabolism, but also highlight the potential role of specific lipoproteins in atherogenesis. (<i>JAMA</i>. 1991;265:78-83)
Sacrococcygeal Teratoma in a Neonate
Authors: G. Frederick Worsham
Journal: JAMA (1978)

ACETAZOLAMIDE, a carbonic anhydrase inhibitor, has well-established teratogenic potential in rats, hamsters, and mice.<sup>1,2</sup>According to a July 17, 1975, letter from L. Lizabeth Monroe, MD, of the Lederle Laboratories, Pearl River, NY, there is only one known case of an infant with congenital anomalies (including congenital glaucoma, microophthalmia, and patent ductus arteriosus) born to a mother treated throughout pregnancy with acetazolamide. <h3>Report of a Case</h3> A 22-year-old woman, gravida 2, para 0, abortus 1, was admitted to the National Naval Medical Center at 27 weeks' gestation, with spontaneous rupture of the membranes. The patient had had glaucoma since an episode of bilateral uveitis at age 13 years. She had been treated with acetazolamide, 750 mg daily, continuously since that time and had required enucleation of the left eye at age 17 years. Acetazolamide therapy was discontinued at 19 weeks' gestation. Other medications were ones without known teratogenic effects
What Has Genomics Taught an Evolutionary Biologist?
Authors: Jianzhi Zhang
Journal: Genomics Proteomics & Bioinformatics (2023)

Genomics, an interdisciplinary field of biology on the structure, function, and evolution of genomes, has revolutionized many subdisciplines of life sciences, including my field of evolutionary biology, by supplying huge data, bringing high-throughput technologies, and offering a new approach to biology. In this review, I describe what I have learned from genomics and highlight the fundamental knowledge and mechanistic insights gained. I focus on three broad topics that are central to evolutionary biology and beyond-variation, interaction, and selection-and use primarily my own research and study subjects as examples. In the next decade or two, I expect that the most important contributions of genomics to evolutionary biology will be to provide genome sequences of nearly all known species on Earth, facilitate high-throughput phenotyping of natural variants and systematically constructed mutants for mapping genotype-phenotype-fitness landscapes, and assist the determination of causality in evolutionary processes using experimental evolution.
The Presence of Typical “BRAFV600E-Like” Atypia in Papillary Thyroid Carcinoma is Highly Specific for the Presence of the BRAFV600E Mutation
Authors: John Turchini, Loretta Sioson, Adele Clarkson, Amy Sheen, Leigh Delbridge, Anthony Glover, Mark Sywak, Stan Sidhu, Anthony J. Gill
Journal: Endocrine Pathology (2023)
A Phase 1 Trial of Durvalumab in Combination with Bacillus Calmette-Guerin (BCG) or External Beam Radiation Therapy in Patients with BCG-unresponsive Non-muscle-Invasive Bladder Cancer: The Hoosier Cancer Research Network GU16-243 ADAPT-BLADDER Study
Authors: Noah M. Hahn, Michael A. O'Donnell, Jason A. Efstathiou, Marianna Zahurak, Gary L. Rosner, Jeff Smith, Max R. Kates, Trinity J. Bivalacqua, Phuoc T. Tran, Daniel Y. Song, Alex S. Baras, Andres Matoso, Woonyoung Choi, Kellie N. Smith, Drew M. Pardoll, Luigi Marchionni, Bridget McGuire, Mary Grace Phelan, Burles A. Johnson, Tanya O'Neal, David J. McConkey, Tracy L. Rose, Marc Bjurlin, Emerson A. Lim, Charles G. Drake, James M. McKiernan, Israel Deutsch, Christopher B. Anderson, Donald L. Lamm, Daniel M. Geynisman, Elizabeth R. Plimack, Mark A. Hallman, Eric M. Horwitz, Essel Al-Saleem, David Y.T. Chen, Richard E. Greenberg, Alexander Kutikov, Gordon Guo, Timothy A. Masterson, Nabil Adra, Hristos Z. Kaimakliotis
Journal: European Urology (2023)
Re: Maria S. Lindgren, Eric Hansen, Nessn Azawi, Anna M. Nielsen, Lars Dyrskjøt, Jørgen B. Jensen. DaBlaCa-13 Study: Oncological Outcome of Short-term, Intensive Chemoresection with Mitomycin in Nonmuscle Invasive Bladder Cancer: Primary Outcome of a Randomized Controlled Trial. J Clin Oncol. In press. https://doi.org/10.1200/JCO.22.00470
Authors: Benjamin Pradere, Giuseppe Basile, Thomas Seisen
Journal: European Urology (2023)